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Table 2 Nine SNPs selected for functional evaluation

From: Multiple regulatory variants located in cell type-specific enhancers within the PKP2 locus form major risk and protective haplotypes for canine atopic dermatitis in German shepherd dogs

SNP SNP 27:18,861,228 SNP 27:19,086,778 SNP 27:19,093,355 SNP 27:19,096,199 SNP 27:19,112,169 SNP 27:19,114,170 SNP 27:19,124,996 SNP 27:19,135,677 SNP 27:19,140,837 Haplotype ID GSD cases (%) a GSD controls (%) a p-valueb OR
Control alleles C C C T A C T G T 5 84.6 97.6 0.0032 0.14 (95 CI: 0.03–0.6)
Risk alleles A T T G G G A A G 20 35.2 9.6 5.9×10−5 5.1 (95 CI: 2.2–11.9)
Association p-value in GSD 1.3×10−5 2.7×10−6 7.1×10−5 2.8×10−5 1.9×10−5 1.9×10−5 3.8×10−6 1.0×10−5 2.7×10−6      
Rank in association analyses:               
GWAS 2 na na na na na na na 1      
GSD fine-map 16 1 37 26 21 20 3 12 1      
GSD + LRCAD breeds 64 1 9 4 2 3 14 1 15      
  1. Haplotype 5 was present in GSD, Boxer, Smalands hound, Golden retriever, Bull terrier, Elkhound, Hovawart, Giant Schnauzer, Irish wolfhound, Irish soft-coated wheaten terrier, and Wachtelhund
  2. Haplotype 20 was present in GSD, Labrador and Golden retriever
  3. a Dogs either heterozygous or homozygous for the allele in %
  4. b Fisher’s Exact probability test, two-tailed